GROMACS version: 2020
GROMACS modification: No
Hello Friends,
I have a long simulation, and I want to automatically choose representative structures (clustering). By following this tutorial, I have
#since it is a long trajectory, I take one frame every 100
gmx trjconv -f md_prod_nopbc.xtc -skip 100 -o md_prod_nopbc_reduced.xtc
#I call rms with f and f2, indicating that I want to compare two trajectories (in my case, a trajectory with itself), and that it should generate the xpm file rmsd_matrix.xpm
echo -e "Backbone\nBackbone" | gmx rms -f md_prod_nopbc_reduced.xtc -f2 md_prod_nopbc_reduced.xtc -s md_prod.tpr -m rmsd_matrix.xpm
#finally, I TRY to convert the xpm file to eps
gmx xpm2ps -f rmsd_matrix.xpm -o rmsd_matrix.eps
But I am greeted with the following error
-------------------------------------------------------
Program: gmx xpm2ps, version 2020
Source file: src/gromacs/fileio/matio.cpp (line 297)
Input error or input inconsistency:
Invalid XPixMap
In fact, I cannot use any command that uses a xpm file, such as gmx cluster (I can use this command but without the precalculated xpm matrix, and thus it has to calculate it again).
The fun thing is that I can open the xpm matrix with GIMP and it is fine. I am very puzzled by this error, even more because there is not a single record on the web of anyone else having the same problem.
I hereby “attach” the xpm file in question. I would be very very grateful to anyone who could download my xpm, and then run
gmx xpm2ps -f rmsd_matrix.xpm -o rmsd_matrix.eps
and tell me if it fails or not
Kind regards